SMTL ID : 4q6n.1

Structural analysis of the tripeptide-bound form of Helicobacter pylori Csd4, a D,L-carboxypeptidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x MHI: L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID(Non-covalent)

MHI.1: 16 residues within 4Å: Chain A: R.85, N.92, R.93, H.125, H.127, G.129, G.130, W.147, M.202, A.205, L.206, T.207, A.219, E.221, K.224 Ligands: CA.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:W.147, A:W.147, A:A.219 Hydrogen bonds: A:R.85, A:N.92, A:G.130, A:L.206, A:T.207, A:T.207, A:E.221 Water bridges: A:Q.45, A:Q.45, A:R.85, A:R.93, A:R.93, A:R.146, A:W.147, A:D.154, A:T.195, A:T.207, A:F.208, A:K.224, A:K.224 Salt bridges: A:R.93, A:H.125, A:H.127, A:K.224

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: Q.45, E.48, R.85, H.127 Ligands: MHI.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.48, A:E.48, A:H.127, H2O.1, H2O.8 CA.3: 4 residues within 4Å: Chain A: N.381, V.382, F.385, E.395 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.382, A:F.385, A:E.395, H2O.3, H2O.6 CA.4: 2 residues within 4Å: Chain A: H.61, D.253 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.61, A:D.253, A:D.253, H2O.17

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.252, D.253, F.254, D.255 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.255 Water bridges: A:D.255 GOL.6: 4 residues within 4Å: Chain A: F.250, K.251, R.252 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.252, A:R.252 Water bridges: A:E.240, A:F.250, A:F.250 GOL.7: 3 residues within 4Å: Chain A: N.244, Q.245, N.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.245, A:N.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H.S. et al., Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-11-05

Peptides

Conserved hypothetical secreted protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Conserved hypothetical secreted protein

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